Computational protocol: PCR-RFLP assay as an option for primary HPV test

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Protocol publication

[…] DNA sequencing of PGMY09/11 PCR fragments was performed for samples with discordant results between the two genotyping methods. The amplicons were purified with the PureLink® PCR Purification kit (Life Tecnologies™, Germany) or with QIAquick Gel Extraction kit (Qiagen), according to the manufacturers' instructions. Automated DNA sequencing was performed in an ABI 3730 Genetic Analyzer sequencer (Applied Biosystems, USA). The accuracy of the DNA sequencing was evaluated through the CAP3 program based on Phred quality score ().Sequences were aligned and compared to those available in the GenBank database using the software Chromas Lite 2.1 (Technelysium, Australia). HPV type was identified based on >90% sequence homology over 449–458 nucleotides. […]

Pipeline specifications

Software tools CAP3, Chromas
Application Sanger sequencing
Organisms Human papillomavirus, Homo sapiens, Human papillomavirus type 16
Diseases Neoplasms, Papilloma, HIV Infections